ArticleJournal of molecular biology2014
Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins.
Article in Journal of molecular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Droplet growth, Ostwald's rule, and emergence of order in Fused in Sarcoma.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Understanding domain swapping in the c-Src SH3 domain through hinge-loop mutagenesis.Acta crystallographica. Section D, Structural biology · 2025Article
- Exploring the unfolding pathways of protein families using Elastic Network Model.Scientific reports · 2024Article
- Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain.Biopolymers · 2024Review
- Article
- Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages.Science advances · 2023Article
- Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The intriguing dose-dependent effect of selected amphiphilic compounds on insulin amyloid aggregation: Focus on a cholesterol-based detergent, Chobimalt.Frontiers in molecular biosciences · 2022Article
- Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants.The journal of physical chemistry letters · 2021Article
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
- Differences in the free energies between the excited states of AProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Causative Links between Protein Aggregation and Oxidative Stress: A Review.International journal of molecular sciences · 2019Review
- Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states.The Journal of chemical physics · 2018Article
- Soft Vibrational Modes Predict Breaking Events during Force-Induced Protein Unfolding.Biophysical journal · 2018Article
- Understanding protein domain-swapping using structure-based models of protein folding.Progress in biophysics and molecular biology · 2017Review
- Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model.Physical chemistry chemical physics : PCCP · 2017Article
- SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies.Journal of computational chemistry · 2016Article
- Reply to Alberti: Are in vitro folding experiments relevant in vivo?Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Force-dependent switch in protein unfolding pathways and transition-state movements.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
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Authors and funding
4 authors.
Funding
Abstract
Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N(⁎)) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration ([C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N(⁎) states. Interestingly, the phase boundaries separating the folded and unfolded states at all [C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N(⁎) with a disordered solvent-exposed amino-terminal β-strand. The structure of the N(⁎) state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N(⁎) state, determined by the free energy gap separating the native structure and the N(⁎) state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N(⁎) state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain.
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